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Low expression levels RNA-seq data filtering
Question
ID
112
Category
Qlucore Omics Explorer
  Analysis
Date Created
2015-09-21 11:45:40
Date Updated
2015-09-21 11:48:12
How to filter away genes with low expression levels from RNA-seq data?
Answer
This is applicable to data that has been imported as BAM-files into Qlucore Omics Explorer.

The data are represented on the log2(FPKM) scale, incorporating TMM normalization factors in the between-sample normalization step.

1.Set the threshold in the data tab to 0 (will be automatically changed to 1e-6). This will exchange all values below this value to 1e-6.

2. Perform a minimum variance filtration, by moving the variance slider in the statistics dialogue a minimum step to the right. This will remove all genes where all results are the same (e.g. 1e-6).

3. Save a list of the remaining genes.

4. Remove the threshold in order to restore the original values for the remaining genes.

5.Use the list as input in your analysis. (You can save this as a new gedata-file, where you select the option to only save the active variables.)

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